Table 1 |
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|
Comparison of mapping efficiencies and estimation of methylation levels in various genomic contexts |
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|
BatMeth (%) |
Bismark (%) |
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|
|
|
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|
Mapping efficiency |
CG |
CHG |
CHH |
Mapping efficiency |
CG |
CHG |
CHH |
Oracle BS rate (%) |
|
|
||||||||
|
94.2 |
0.0 |
0.0 |
0.0 |
91.1 |
0.0 |
0.0 |
0.0 |
0.0 |
|
94.0 |
10.0 |
10.0 |
10.0 |
92.1 |
10.0 |
10.0 |
10.0 |
10.0 |
|
93.9 |
20.0 |
20.0 |
20.0 |
92.4 |
20.0 |
20.1 |
20.0 |
20.0 |
|
93.8 |
30.0 |
30.0 |
30.0 |
92.5 |
29.9 |
30.0 |
30.0 |
30.0 |
|
93.6 |
39.9 |
40.0 |
40.0 |
92.5 |
40.0 |
40.0 |
40.0 |
40.0 |
|
93.5 |
50.0 |
50.0 |
50.0 |
92.6 |
50.0 |
50.0 |
50.0 |
50.0 |
|
93.4 |
60.0 |
60.0 |
60.0 |
92.6 |
60.0 |
60.1 |
60.0 |
60.0 |
|
93.2 |
70.0 |
70.0 |
70.0 |
92.7 |
70.0 |
70.0 |
70.0 |
70.0 |
|
93.0 |
79.9 |
80.0 |
80.0 |
92.6 |
79.9 |
80.0 |
80.0 |
80.0 |
|
92.8 |
90.0 |
90.0 |
90.0 |
92.6 |
90.1 |
90.0 |
90.0 |
90.0 |
|
92.6 |
100 |
100.0 |
100.0 |
92.6 |
100.0 |
100.0 |
100.0 |
100.0 |
|
|
||||||||
|
Methylation levels in various genomic contexts, such as CG, CHG and CHH (H is A/C/T only), are called by BatMeth and Bismark and validated against the oracle bisulfite rate used in Sherman. |
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|
Lim et al. Genome Biology 2012 13:R82 doi:10.1186/gb-2012-13-10-r82 |
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